MarkDuplicates analysis of large wheat chromosomes

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John Baison

• November 11, 2021 11:54

I am working with the wheat genome and I am seeing the following warning when marking duplicates

WARNING 2021-11-11 12:37:03 BAMRecordCodec Reference length is too large for BAM bin field.
WARNING 2021-11-11 12:37:03 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0.

Is there a work around in order to mark duplicates on the large wheat chromosomes?

 

Regards,

John.

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  Genevieve Brandt (she/her)

  • November 12, 2021 19:16

  Hi John,

  Could you share your entire command, stack trace, and GATK version? We did have a somewhat similar issue come up with the wheat genome and MarkDuplicates but I don't have enough information about your case to know if there is a good workaround.

  Best,

  Genevieve

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  Miriam Marin Sanz

  • February 23, 2023 08:46

  Hi Genevieve,

   

  We have also the same problem with the durum wheat genome.

  Warning messages:

  WARNING 2023-02-23 09:22:48     BAMRecordCodec  Reference length is too large for BAM bin field.
  WARNING 2023-02-23 09:22:48     BAMRecordCodec  Reads on references longer than 536870912bp will have bin set to 0.

   

  The command was:

  gatk MarkDuplicates -I sample.sorted.bam -M sample_dedup_metrics.txt -O sample_sorted_dedup.bam

  GATK version:

  The Genome Analysis Toolkit (GATK) v4.3.0.0
  HTSJDK Version: 3.0.1
  Picard Version: 2.27.5

   

  Thank you in advance,

  Miriam

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